Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.46 kDa 
• Atom Count: 2299 
• Modelled Residue Count: 262 
• Deposited Residue Count: 292 
• Unique protein chains: 4

2HNT

CRYSTALLOGRAPHIC STRUCTURE OF HUMAN GAMMA-THROMBIN

• DOI: 10.2210/pdb2HNT/pdb

• Classification: SERINE PROTEASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1994-08-23 Released: 1994-11-30 
• Deposition Author(s): Tulinsky, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 0.156 

Literature

Crystallographic structure of human gamma-thrombin.

Rydel, T.J., Yin, M., Padmanabhan, K.P., Blankenship, D.T., Cardin, A.D., Correa, P.E., Fenton 2nd., J.W., Tulinsky, A.

(1994) J Biol Chem 269: 22000-22006

• PubMed: 8071320 
• Primary Citation of Related Structures:  
  2HNT


• PubMed Abstract: 
  

In an effort to prepare crystals and determine the structure of alpha-thrombin complexed to a synthetic peptide inhibitor (MDL-28050) of the hirudin 54-65 COOH-terminal region, it was discovered that the crystals were not those of the complex but of gamma-thrombin. Gel electrophoresis studies revealed that autolytic degradation had occurred prior to crystallization. NH2-terminal sequence analysis of these autolytic fragments confirmed the gamma-thrombin product (cleavages at Arg75-Tyr76 and/or Arg77A-Asn78, and Lys149E-Gly150; chymotrypsinogen numbering) with a minor amount of another autolysis product, beta-thrombin (first two cleavages only). The final structure has an R-factor of 0.156 for 7.0-2.5-A data, and includes 186 water molecules. A comparison of gamma-thrombin with the thrombin structure in the alpha-thrombin-hirugen complex revealed that the two structures agreed well (r.m.s. delta = 0.39 A for main chain atoms). These structures possess uninhibited active sites where the disposition of the catalytic triad residues is nearly identical. The electron density in the vicinity of the gamma-thrombin cleavage regions is poor, and only becomes well-defined several residues prior to and after the actual cleavage sites. The extensive disorder evoked by beta-cleavage(s) in the Lys70-Glu80 loop region indicates that this part of the molecule is severely disrupted by autolysis and is the reason exosite functions are dramatically impaired in beta-and gamma-thrombin. Since autolysis did not lead to a major reorganization of the folded structure of alpha-thrombin, the likely structural features of the interaction of thrombin substrate with thrombin enzyme during beta-cleavage have been modeled by docking the exosite region of one molecule at the active site of another.

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Related Citations: 

• Refined Structure of the Hirudin-Thrombin Complex
  Rydel, T.J., Tulinsky, A., Bode, W., Huber, R.
  (1991) J Mol Biol 221: 583

• Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin
  Skrzypczak-Jankun, E., Carperos, V.E., Ravichandran, K.G., Tulinsky, A., Westbrook, M., Maraganore, J.M.
  (1991) J Mol Biol 221: 1379

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Organizational Affiliation: 

Department of Chemistry, Michigan State University, East Lansing 48824-1322.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA-THROMBIN	A [auth L]	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA-THROMBIN	B [auth C]	70	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA-THROMBIN	C [auth E]	81	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA-THROMBIN	D [auth F]	105	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 0.156 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.45	α = 90
b = 48.23	β = 96.2
c = 52.43	γ = 90

Software Package:

Software Name	Purpose
PROFFT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-08-23 
• Released Date: 1994-11-30 
Deposition Author(s): Tulinsky, A.

Revision History  

• Version 1.0: 1994-11-30
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance